Locus 1786

Sequence ID	X_DroMel_CAF1
Location	4,935,208 – 4,935,410
Length	202
Max. P	0.953970

overview

Window 7

Location	4,935,208 – 4,935,316
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.43
Mean single sequence MFE	-32.58
Consensus MFE	-25.04
Energy contribution	-24.43
Covariance contribution	-0.61
Combinations/Pair	1.23
Mean z-score	-2.34
Structure conservation index	0.77
SVM decision value	1.44
SVM RNA-class probability	0.953970
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4935208 108 + 22224390
------AAACCGUG---C---ACCAAAAUGGCGGACAUCAUGCGUCCGCCGUACAGUGAGAUCAAACGGCCGGACGAAAUCGUCAGAAUGACAACCGCCGACAAUCUCAAGUUCGCCGUC
------....((.(---(---......(((((((((.......)))))))))....((((((....((((.((..(....)(((.....)))..))))))...)))))).....)))).. ( -36.00)
>DroVir_CAF1 9402 104 + 1
CUCG-------------A---UACAAAAUGGCGGACAUCAUGCGUCCGCCGUUUAGCGACAUUAAGCGGCCCGACGAAAUUGUCAGAAUGACGACCGCCGACAAUCUCAAAUUUGCCGUC
.(((-------------.---....(((((((((((.......)))))))))))..)))......(((((..((((....))))(((.((.((.....)).)).))).......))))). ( -31.50)
>DroGri_CAF1 11855 108 + 1
CUCCAAAA---------A---UACAAAAUGGCGGACAUCAUGCGUCCGCCGUACAGCGAUAUAAAGCGGCCCGACGAAAUUGUCAGAAUGACAACCGCCGAUAAUUUGAAAUUCGCCGUA
........---------.---......(((((((((.......)))))))))((.((((..((((.((((.........(((((.....)))))..))))....))))....)))).)). ( -30.20)
>DroSim_CAF1 2 95 + 1
-------------------------AAAUGGCGGACAUCAUGCGUCCGCCGUACAGUGAGAUCAAACGGCCGGACAAAAUCGUCAAAAUGACAACCGCCGACAAUCUCAAGUUCGCCGUC
-------------------------..(((((((((.....(((((((((((....((....)).)))).)))))......(((.....)))....)).((.....))..))))))))). ( -32.30)
>DroWil_CAF1 8230 117 + 1
CAC---AAAAACUUCAACGCAAACAAAAUGGCGGACAUCAUGCGUCCGCCGUUUAGUGAGAUCAAACGGCCGGAUGAGAUUGUCAGAAUGACAACCGCCGAUAACUUGAAAUUUGCCGUC
...---............((((((.(((((((((((.......))))))))))).)).........((((.((......(((((.....)))))))))))............)))).... ( -33.70)
>DroMoj_CAF1 12889 104 + 1
CUCG-------------U---UACAAAAUGGCGGACAUCAUGCGUCCGCCGUUCAGCGACAUUAAGCGGCCCGACGAAAUCGUCAGAAUGACAACCGCCGAUAAUCUGAAAUUUGCCGUC
...(-------------(---..(..((((((((((.......))))))))))..)..)).....(((((..((((....))))(((.((.(.......).)).))).......))))). ( -31.80)
>consensus
CUC______________A___UACAAAAUGGCGGACAUCAUGCGUCCGCCGUACAGCGAGAUCAAACGGCCCGACGAAAUCGUCAGAAUGACAACCGCCGACAAUCUCAAAUUCGCCGUC
...........................(((((((((.......))))))))).............(((((..((((....)))).((((.....................))))))))). (-25.04 = -24.43 +  -0.61)

alignment

secondary structure

dotplot

Window 8

Location	4,935,208 – 4,935,316
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.43
Mean single sequence MFE	-37.59
Consensus MFE	-27.69
Energy contribution	-27.25
Covariance contribution	-0.44
Combinations/Pair	1.17
Mean z-score	-2.05
Structure conservation index	0.74
SVM decision value	1.20
SVM RNA-class probability	0.930234
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4935208 108 - 22224390
GACGGCGAACUUGAGAUUGUCGGCGGUUGUCAUUCUGACGAUUUCGUCCGGCCGUUUGAUCUCACUGUACGGCGGACGCAUGAUGUCCGCCAUUUUGGU---G---CACGGUUU------
..(((((.((.((((((((((((((((((((.....))))))..)).))))).....)))))))..)).)((((((((.....))))))))........---)---).))....------ ( -40.30)
>DroVir_CAF1 9402 104 - 1
GACGGCAAAUUUGAGAUUGUCGGCGGUCGUCAUUCUGACAAUUUCGUCGGGCCGCUUAAUGUCGCUAAACGGCGGACGCAUGAUGUCCGCCAUUUUGUA---U-------------CGAG
((..(((((...(((((((((((..(....)...)))))))))))((..(((.((.....)).)))..))((((((((.....))))))))..))))).---)-------------)... ( -36.70)
>DroGri_CAF1 11855 108 - 1
UACGGCGAAUUUCAAAUUAUCGGCGGUUGUCAUUCUGACAAUUUCGUCGGGCCGCUUUAUAUCGCUGUACGGCGGACGCAUGAUGUCCGCCAUUUUGUA---U---------UUUUGGAG
((((((((...........((((((((((((.....))))))..))))))...........)))))))).((((((((.....))))))))........---.---------........ ( -38.65)
>DroSim_CAF1 2 95 - 1
GACGGCGAACUUGAGAUUGUCGGCGGUUGUCAUUUUGACGAUUUUGUCCGGCCGUUUGAUCUCACUGUACGGCGGACGCAUGAUGUCCGCCAUUU-------------------------
.((((.((...(.((((.(((((((((((((.....))))))..)).))))).)))).)..)).))))..((((((((.....))))))))....------------------------- ( -35.40)
>DroWil_CAF1 8230 117 - 1
GACGGCAAAUUUCAAGUUAUCGGCGGUUGUCAUUCUGACAAUCUCAUCCGGCCGUUUGAUCUCACUAAACGGCGGACGCAUGAUGUCCGCCAUUUUGUUUGCGUUGAAGUUUUU---GUG
.((((.(((((((((......((((((((((.....))))))).......((((((((.......))))))))(((((.....)))))))).....(....).)))))))))))---)). ( -36.60)
>DroMoj_CAF1 12889 104 - 1
GACGGCAAAUUUCAGAUUAUCGGCGGUUGUCAUUCUGACGAUUUCGUCGGGCCGCUUAAUGUCGCUGAACGGCGGACGCAUGAUGUCCGCCAUUUUGUA---A-------------CGAG
..(((((((.(((((..(((.((((((.......((((((....))))))))))))..)))...))))).((((((((.....))))))))..))))).---.-------------)).. ( -37.91)
>consensus
GACGGCAAAUUUCAGAUUAUCGGCGGUUGUCAUUCUGACAAUUUCGUCCGGCCGCUUGAUCUCACUGAACGGCGGACGCAUGAUGUCCGCCAUUUUGUA___G______________GAG
..((((..((........)).((((((((((.....))))))..))))..))))................((((((((.....))))))))............................. (-27.69 = -27.25 +  -0.44)

alignment

secondary structure

dotplot

Window 9

Location	4,935,316 – 4,935,410
Length	94
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	75.41
Mean single sequence MFE	-29.77
Consensus MFE	-19.59
Energy contribution	-19.57
Covariance contribution	-0.03
Combinations/Pair	1.25
Mean z-score	-1.45
Structure conservation index	0.66
SVM decision value	0.77
SVM RNA-class probability	0.845348
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4935316 94 + 22224390
CUCAUUGGCCUCAUCGAGGUUGGCCAGGUGACCAACCGGGAGGUGGUCAACACCGUUCUGCAUUUGGUAAGUGCUAGU---UACAGCCAAUUAGCCG
......((((((...)))((((((..((((((((.((....)))))))...)))((.(((((((.....))))).)).---.)).))))))..))). ( -31.00)
>DroGri_CAF1 11963 74 + 1
CUCAUCGGCCUCAUCGAGGUUGGCCAGGUGACCAAUCGGGAGGUGGUCAACACCGUGUUACAUUUGGUAAGUGU-----------------------
.....(((((((...)))))))((((((((.((....))..((((.....))))......))))))))......----------------------- ( -25.30)
>DroEre_CAF1 9622 93 + 1
CUCAUCGGCCUCAUCGAGGUUGGCCAGGUGACCAACCGGGAGGUGGUGAACACCGUUCUGCAUUUGGUAAGUGCCAGC---AGC-GCUAGUCAGCCG
....((((.....))))(((((((..((((((((.((....))))))...))))((.((((...((((....))))))---)).-))..))))))). ( -35.00)
>DroWil_CAF1 8347 92 + 1
CUCAUCGGCCUAAUCGAGGUGGGCCAGGUGACCAAUCGUGAGGUGGUCAAUACUGUGUUACAUUUGGUAAGUACCCAUAUGAAUAA-----CUACUU
......((((((.......))))))((.((((((.((....))))))))...))(((((((((.(((.......))).)))..)))-----).)).. ( -26.70)
>DroYak_CAF1 9092 77 + 1
CUCAUCGGCCUUAUCGAGGUUGGCCAGGUGACCAACCGGGAGGUGGUCAACACCGUGCUGCAUUUGGUAAGUGCCAC--------------------
......((((((((((((...(((..((((((((.((....)))))))...)))..)))...))))))))).)))..-------------------- ( -32.20)
>DroPer_CAF1 8575 91 + 1
CUCAUCGGCCUCAUCGAGGUGGGGCAGGUCACCAACCGCGAGGUUGUGAACACCGUACUGCAUUUGGUAAGUGCUAUU---UAUAA---AAUAAUCU
.......(((((((....))))))).((((((.((((....))))))))...))(((((((.....)).)))))....---.....---........ ( -28.40)
>consensus
CUCAUCGGCCUCAUCGAGGUUGGCCAGGUGACCAACCGGGAGGUGGUCAACACCGUGCUGCAUUUGGUAAGUGCCAGU____A_________A_CC_
......(((((.((((((((.(..(.(.((((((.((....))))))))...).)..).)).)))))).)).)))...................... (-19.59 = -19.57 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:52 2006